Journal of Membrane Biology

, Volume 235, Issue 1, pp 43–50 | Cite as

Comparing Membrane Simulations to Scattering Experiments: Introducing the SIMtoEXP Software

Article

Abstract

SIMtoEXP is a software package designed to facilitate the comparison of biomembrane simulations with experimental X-ray and neutron scattering data. It has the following features: (1) Accepts number density profiles from simulations in a standard but flexible format. (2) Calculates the electron density ε(z) and neutron scattering length density ν(z) profiles along the z direction (i.e., normal to the membrane) and their respective Fourier transforms (i.e., F ε [q z ] and F ν [q z ]). The resultant four functions are then displayed graphically. (3) Accepts experimental F ε (q z ) and F ν (q z ) data for graphical comparison with simulations. (4) Allows for lipids and other large molecules to be parsed into component groups by the user and calculates the component volumes following Petrache et al. (Biophys J 72:2237–2242, 1997). The software then calculates and displays the contributions of each component group as volume probability profiles, ρ(z), as well as the contributions of each component to ε(z) and ν(z).

Keywords

MD simulation X-ray scattering Neutron scattering Computer software 

Notes

Acknowledgements

We thank Scott Feller, Jonathan Sachs, Jason Perlmutter and Jeffery Klauda for providing us with simulation data, and Olle Edholm and Frank Heinrich for valuable feedback. N. K. acknowledges partial funding from the Advanced Foods and Materials Network (AFMNet), a Network of Centres of Excellence of Canada. J. F. N. was supported by the U.S. National Institutes of Health, Institute of General Medicine (grant GM44976).

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Copyright information

© Her Majesty the Queen in Right of UK 2010

Authors and Affiliations

  • Norbert Kučerka
    • 1
    • 2
  • John Katsaras
    • 1
    • 3
    • 4
  • John F. Nagle
    • 5
    • 6
  1. 1.Canadian Neutron Beam CentreNational Research CouncilChalk RiverCanada
  2. 2.Department of Physical Chemistry of Drugs, Faculty of PharmacyComenius UniversityBratislavaSlovakia
  3. 3.Guelph-Waterloo Physics Institute and Biophysics Interdepartmental GroupUniversity of GuelphGuelphCanada
  4. 4.Department of PhysicsBrock UniversityCatharinesCanada
  5. 5.Department of PhysicsCarnegie Mellon UniversityPittsburghUSA
  6. 6.Department of Biological SciencesCarnegie Mellon UniversityPittsburghUSA

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